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[188662_at] Rhomboid

Description C48B4.2 /REP_DB=WormBase Gene ID /WP=CE00492 /TR=SW:P34356 /GB=CAA82377.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Rhomboid
Cluster 6grp_highest_10_10 > 41      6grp_high1_10_10 > 14      4grp_highest_8_8 > 62      4grp_high_8_8 > 18      6grp_highest_nonorm > 80      6grp_total > 14      4grp_total > 30      6grp_highest_sub > De      6grp_cgc > 41      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 185
1 2 3 4 range
A 299.8
(3)
P 		263.7
(1.8)
P 		114.7
(-3)
P 		209
(0.1)
P 		185
B 297.2
(3)
P 		202.8
(-1.5)
P 		171.5
(-3)
P 		231.5
(-0.1)
P 		126
C 251.8
(1.9)
P 		169.1
(-2.4)
P 		158.6
(-3)
P 		272.7
(3)
P 		114
avr 282.9
(3) 		211.9
(-0.2) 		148.3
(-3) 		237.7
(1) 		135

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 173
1 2 3 4 5 6 range
A 291.5
(2.2)
P 		306.4
(3)
P 		255.9
(0.4)
P 		226.9
(-1.1)
P 		200.3
(-2.4)
P 		188.9
(-3)
P 		118
B 276.8
(3)
P 		242.4
(1.6)
P 		133.5
(-3)
P 		247.2
(1.8)
P 		179.3
(-1.1)
P 		201
(-0.2)
P 		143
C 257.4
(3)
P 		250.5
(2.6)
P 		240.1
(2)
P 		200.4
(-0.4)
P 		195.7
(-0.7)
P 		156.7
(-3)
P 		101
avr 275.2
(3) 		266.4
(2.4) 		209.8
(-1.2) 		224.8
(-0.3) 		191.8
(-2.4) 		182.2
(-3) 		93
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 79
1 2 3 4 range
A 109.2
(3)
P 		57.2
(-0.9)
P 		30
(-3)
P 		30.6
(-3)
P 		79
B 94.8
(3)
P 		50.1
(-1.9)
P 		39.7
(-3)
P 		49.3
(-2)
P 		55
C 83.4
(3)
P 		48.6
(-2.6)
P 		55.3
(-1.5)
P 		46
(-3)
P 		37
avr 95.8
(3) 		52
(-1.9) 		41.7
(-3) 		42
(-3) 		54

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 77
1 2 3 4 5 6 range
A 53.7
(-2.3)
P 		109
(3)
P 		55.7
(-2.1)
P 		57.5
(-1.9)
P 		60.4
(-1.6)
P 		46
(-3)
P 		63
B 96.3
(3)
P 		80.7
(1.5)
P 		32.4
(-3)
P 		65.5
(0.1)
P 		72.8
(0.8)
P 		74.9
(1)
P 		64
C 95.4
(3)
P 		76.4
(0.9)
P 		61.1
(-0.7)
P 		40.3
(-3)
P 		63.3
(-0.5)
P 		52.5
(-1.7)
P 		55
avr 81.8
(1.9) 		88.7
(3) 		49.7
(-3) 		54.4
(-2.3) 		65.5
(-0.6) 		57.8
(-1.8) 		39
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188662_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6322
Sequence Type Exemplar sequence
Representative Public ID C48B4.2 NCBI
Target Description C48B4.2 /REP_DB=WormBase Gene ID /WP=CE00492 /TR=SW:P34356 /GB=CAA82377.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Rhomboid
Cluster Evidence This cluster is supported by a Sanger Annotation.
Annotation Method Description
Annotation Description This probe set was annotated using the Matching Probes based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade A annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_066719(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066719 NCBI Caenorhabditis elegans C48B4.2 (Rhomboid) mRNA, complete cds. 11/11 None
C48B4.2 ENSEMBL cdna:known chromosome:CEL140:III:9592178:9595470:-1 gene:C48B4.2 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000040768 5/11 Cross Hyb Matching Probes None
GENEFINDER00000040779 8/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:9592173-9595213(-) 100.0 100.0
Public Domain and Genome References
Gene Title Rhomboid
Gene Symbol rom-2
Ensembl C48B4.2
Entrez Gene 183564 Entrez gene
SwissProt P34356 EMBL-EBI
WormBase CE37757 Wormbase
Functional Annotations
Ortholog
ID Title Organism
DROSOPHILA_2:1623692_S_AT rhomboid-4 dm
DROSOPHILA_2:1623158_S_AT rhomboid-4 dm
DROSGENOME1:141678_AT rhomboid-4 dm
Gene Ontology
GO Molecular Function (view graph)
ID Description Evidence Links
5509 calcium ion binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA82377 Hypothetical protein C48B4.2 [Caenorhabditis elegans] ref|NP_499120.2| C48B4.2 [Caenorhabditis elegans] sp|P34356|ROM2_CAEEL Rhomboid related protein 0.0
blast CAE65170 Hypothetical protein CBG10042 [Caenorhabditis briggsae] 0.0
blast XP_395780 PREDICTED: similar to GA14244-PA [Apis mellifera] 3.0E-42
Protein Domains
Database ID Description E-Value
Pfam IPR002048 EMBL-EBI Calcium-binding EF-hand 5.3E-5
Pfam IPR002610 EMBL-EBI Peptidase S54, rhomboid-like protein 3.6E-38
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_499120.2 8 119-141,180-202,209-231,263-285,292-311,321-343,364-386,411-433
C48B4.2 8 119-141,180-202,209-231,263-285,292-311,321-343,364-386,411-433
Sequence
Target Sequence 
>C. ELEGANS:188662_AT
tggaggagcagcgggctcgttttctctcattgcatcacacattacaacaattgcaacaaa
ttttaaagagatggagaatgcaacatgtcgattgccaattcttattgtttttgcggcact
tgactacgttttggcagtttatcaacgattctttgctcccagaattgataaagtgtcaat
gtatggtcatcttggaggccttgtcgccggaattctgttcacattcattttattccgtgg
atccaaaccatcacgattttatactgtttctttttgggtgtcccttgtactttctggatt
ctttatcgccatttgtattactcttattgctgcacccaggactacagttcaagaaattat
taaaaatcagtcattcaaaaataacgcaacacgatgtagtgtgcaaataggaataaactg
tatttcatggacgtctaattttttaatctttgaccacatttttcatgtttcctattccca
tgttcttctcatctctaatgctgtttccaactctctatac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGGAGGAGCAGCGGGCTCGTTTTCT 474 549 594 Antisense
TGCGGCACTTGACTACGTTTTGGCA 347 553 705 Antisense
TGTCGCCGGAATTCTGTTCACATTC 186 557 795 Antisense
ACATTCATTTTATTCCGTGGATCCA 316 105 814 Antisense
GTGGATCCAAACCATCACGATTTTA 109 491 830 Antisense
GGATTCTTTATCGCCATTTGTATTA 536 507 889 Antisense
TTGTATTACTCTTATTGCTGCACCC 456 705 906 Antisense
TGCTGCACCCAGGACTACAGTTCAA 184 583 921 Antisense
TCATGTTTCCTATTCCCATGTTCTT 181 623 1056 Antisense
TCTTCTCATCTCTAATGCTGTTTCC 484 617 1077 Antisense
TAATGCTGTTTCCAACTCTCTATAC 96 637 1089 Antisense
Sequence Source Affymetrix Proprietary Database